Microbial Metabolism
How do pathogens gain energy and nutrients at the cost of patients' health? What do laboratory personnel do when they perform biochemical tests? To identify unknown microorganisms and aid in the diagnosis of disease?
To answer all these questions, it is necessary to know about microbial metabolism. The set of controlled biochemical reactions that take place inside micro-organisms. Although its metabolism is indeed complex.
Involving thousands of chemical reactions and control mechanisms. These reactions are appropriate and can be understood. In this chapter, we will
Equip itself with the central metabolic pathway and energy metabolism.
If you study metabolism. Will be manageable if you keep it in mind. That the ultimate act of metabolism of an organism is the reproduction of the organism. And the process of metabolism is guided by the following eight elementary details:
- Each cell receives mutants that are needed to manufacture chemicals. And generate energy for metabolism.
- Metabolism requires energy from light or the catabolism of acquired nutrients triphosphate.
- Using enzymes, cells break down nutrient molecules. Into primary building blocks called precursor metabolites.
- Use of metabolites, other enzymes, and components of energy older than ATP. Cells perform anabolic reactions.
- Metabolites link the blocks together to form macromolecules. Metamorphosis uses enzymes from ATP and excess energy from ATP.
- Cells grow by combining molecules in connective structures. Such as ribosomes, membranes, and cell walls.
Morphocytes are reproduced once they have doubled in size. We'll discuss each aspect of metabolism in the chapters that apply most. For example, we discussed the first steps of metabolism.
The active and passive forms of transport of nutrients into cells—in Chapter 3. In this chapter, we'll look at catabolism. And Examines the importance of enzymes in anabolic reactions. Studies the three waves involved in synthesizing ATP molecules.
And shows that catabolic and anabolic reactions are linked. Also examines the catabolism of macromolecules. Anabolic reactions in gradients of carbohydrates, lipids, and amino acids. And nucleotides; and some of how cells regulate their metabolic activities.
Basic Chemical Reactions Underlying Metabolism
In the following sections, we will examine the basic concepts of catabolism, and anabolism. And specific classes of reactions such as oxidation-reduction reactions.
In this category, electrons are the transfer of energy between molecules. We will consider ATP and the storage of energy from it. First, we'll make metabolism possible.
Catabolism and Anabolism
Reactions o. A. P. molecules some of which are stored in ATP molecules, although most of the energy is lost as heat. Anabolic reactions are endergonic. There is also some heat loss in anabolism.
Catabolism products are the building blocks for the anabolic reaction. These reactions produce macromolecules and cellular structures, Edina for cell growth and division.
large molecules into small products, and the anabolic pathway. Which synthesizes large molecules from the small products of catabolism. Although catabolic and anabolic pathways are related in cells. It is useful to study both types of pathways as if they were separate
When catabolism pathways break down large molecules. They release energy, catabolism pathways are exogenous. Cells store this energy in the binding of ATP, although most of the energy is dissipated as heat.
Another consequence of the breakdown of large molecules. Catabolic methods are the production of many small molecules. Some of which are precursor metabolites of the metabolite.
Some organisms, such as Escherichia coli, produce no metabolites of any kind. cannot synthesize everything in their cells. Other organisms must get anabolic building blocks. In the form of nutrients from outside their cells.
Catabolic pathways, but not separate catabolic reactions, produce ATP. An example of a catabolism pathway is the breakdown of lipids into glycerol and fatty acids.
Because energy is needed to build anything. Anabolic pathways are endergonic that is. They need more energy than is released. rules for the anabolic pathway.
The energy required for the anabolic pathway.
Is usually derived from ATP molecules generated during catabolism. An example of an anabolic pathway. Is the synthesis of lipids for cell membranes from glycerol and fatty acids.
To summarize, the metabolic pathway of the cell. The catabolic pathway breaks down the molecular building blocks. And macromolecules in the form of ATP to supply energy.
And the anabolic pathway, which synthesizes the building blocks. And macromolecules necessary for ATP growth and reproduction. use for, include.
Oxidation and Reduction Reactions
Many metabolic reactions involve the transfer of electrons. In which energy is carried from an electron donor to an electron acceptor. Such electron transfers are called oxidation-reduction reactions. , or called redox reactions. It may sound backward but electron acceptors are reduced. Because their gain in electrons reduces their total electrical charge.
Molecules that lose electrons are called oxidizers. Because often their electrons are donated to oxygen atoms. An acronym to help you remember these concepts is Oil Rig: In oxidation, there is a loss; in reduction, there is a gain. is included
Reduction and oxidation reactions always occur because the electron is donated. Each chemical is accepted by another chemical. One chemical is reduced by receiving a part of the hydrogen atom, which is made up of a proton and an electron.
Beneficial Microorganisms An interesting example of microbes. In gold mining is how some prokaryotes can reduce the gold dissolved in the solution.
In contrast, a molecule can be oxidized in three ways: by losing a simple electron. By losing a hydrogen atom, or by gaining an oxygen atom. Organic oxidations often involve the loss of hydrogen atoms. Such reactions are also called dehydrogenation.
Electrons are rarely present in the cytoplasm; instead, they orbit the atomic nucleus. Thus the cell uses electron carrier molecules. To transport electrons from one place to another.
Nicotinamide Adenine Dinucleotide Phosphate, Nicotinamide Adenine Dinucleotide Phosphate, and also flavin adenine dinucleotide. Cells use each of these molecules. Specific metabolic pathways carry specific electron pairs. Nad or Nad + A. D.A.
One of the electrons carried by a hydrogen atom is called a 'nad' or nad. Fed has two electrons in the form of hydrogen atoms. Many metabolic pathways, such as those that synthesize ATP, use electron carriers. molecules are required.
ATP Production and Energy Storage
Nutrients contain energy, but that energy is diffused in their chemical bonds. And usually not in enough concentration for use in anabolic reactions. During catabolism, organisms remove energy from nutrients. That can be concentrated and stored in molecules such as ATP. Can be done. This is a normal process called.
cation in which inorganic phosphate (PO3) is added to the substrate. For example, cells convert phosphorus to adenosine diphosphate (ADP). Which has two phosphate groups, to form adenosine triphosphate. Which has There are three phosphate groups.
As we'll examine in the following sections, cells. Phosphorylate ADP makes ATP in three distinct ways:
- Subcellular level phosphorylation. Which involves the transfer of phosphate from another phosphorylated organic compound
- Oxidative phosphorus in which the energy from the redox reaction of respiration. Is used to link inorganic phosphate to ADP.
- Photophosphorylation in which light energy is applied to inorganic phosphates
We'll examine each in detail as we move through the lesson.
APP is then used to generate phosphorylated ATP. Some of the energy of ATP is by breaking phosphate bonds by an anabolic method. Thus, the cyclic interval of APP and ATP functions somewhat like rechargeable batteries.
Rechargeable Batteries ATP molecules store energy from light. And drive cellular processes by extracting energy from catabolic reactions. ADP molecules can be converted back into ATP. Can be "recharged" again.
Role of Enzymes in Metabolism
In catabolic reactions, the bonds must be destabilized before they can be broken. While in anabolic reactions the reactants collide. With enough energy to cause the bonds to form. An increase in ambient temperature produces more chemical reactions.
By increasing the number of collisions. Although neither the repulsive concentration nor. The temperature is high enough to ensure bond formation in living beings. Thus the chemical reactions of life depend on catalysts. .
These are chemicals that increase the likelihood of a reaction. But do not alter the process. Biologicals are called enzymes.
Naming and Classifying Enzymes
Enzyme names usually end with and are often given in the name of each enzyme. Enzyme substrates are molecules that the enzyme acts on. Enzymes can be divided into six basic categories based on their mode of action:
- Hydrolases break down catabolism molecules by adding water. In a decomposition process known as hydrolysis. Ascites
- Fragments are used in the depolymerization of molecules
- Isomerase? Rearrange the atoms inside the molecule, but do not add or remove anything.
- Ligases, or polymerases, link two molecules together (and are thus anabolic). They often use the energy supplied by ATP lyase to split larger molecules (and are thus catabolic). Water is lost in the process. without using.
- Oxidoreductases take electrons out of or take away electrons.
- Transfer functional groups such as an amino group or a phosphate group. Transfers can be anabolic.
Makeup of Enzymes
Many protein enzymes are complete in themselves. But some are composed of both protein and non-protein enzymes.
The proteins in these combinations are called apoenzymes. If one or more non-protein substances are added as cofactors. The apoenzyme is inactivated. The cofactors are either inorganic ions or certain organic molecules called coenzymes.
All coenzymes are either vitamins or contain vitamins. Which are organic molecules that are essential for metabolism. But cannot be synthesized only by mammals. Some bind to inorganic cofactors, some bind to coenzymes, and some combine with both.
The apoenzyme and its cofactor pair to form an active enzyme called the holoenzyme.
There are many examples of inorganic cofactors and organic cofactors. Note that the three main coenzyme electron carriers we see today are Nadal and NAD. And Fed which carries electrons to hydrogen atoms inside cells. We will examine more the roles of these coenzymes in the generation of ATP et.
In eukaryotes, ribozymes process other RNA molecules. By cutting out strands of RNA and joining the remaining fragments together. Recently, researchers. Thus, given that ribosomes make all proteins, ribosomal enzymes enzyme proteins.
Enzyme Activity
Enzymes inside cells catalyze reactions by lowering the activation energy. Which is the amount of energy required to start a chemical reaction. The temperature required for activation.
Is the energy needed to allow cells to survive, so enzymes are needed if metabolism is to occur? This is true even if enzymes are proteins or RNA. N. A. is or the chemical reaction is anabolic or catabolic.
The activity of enzymes depends on the proximity. Between the functional site of the enzyme and its substrate. The size of the functional site of an enzyme. Called its active site, is complementary to the size of the substrate.
The size and location of the nucleotide determine. The conformation of the enzyme's active site. For example, a change in a single component. Makes the enzyme less effective or shuts it down completely.
Enzyme substrate specificity is important for enzyme activity. Has been compared to the fit between a lock and a key. This term is not quite appropriate as enzymes change their shape.
When they bind to their substrate, much like a lock. After insertion, the key is locked into a lock. This latter description of enzymatic substrate specificity is called induced.
In some cases, several different enzymes have active sites. That is complementary to different parts of a single substrate molecule. For the example of Por, a precursor metabolite is called phosphoenolpyruvic acid. Is the substrate for at least five enzymes. Depending on the enzyme involved
Various products are produced from PEP. In the Apache pathway, PEP is converted to pyruvic acid. While in the equilateral anabolic pathway. PEP is converted to the amino acid phenylalanine.
Although the low activation energy of enzymes is not well known. That several mechanisms are in place. Some enzymes bring the reactant close enough to form. While other enzymes change the shape of a reactant. and induce the breaking of a bond. Enzymes increase the likelihood of making or breaking bonds.
The enzyme activities described are following the activation of the enzyme. Which breaks down a molecule called fructose 1, 6-bisphosphate.
- An enzyme associates with a specific substrate molecule whose shape. Is complementary to the active site of the enzyme.
- Intercalation of the substrate induces the enzyme to fit the shape of the substrate.
- The bonds within the substrate are broken, forming two products.
- This is a catabolic reaction; in anabolic reactions. Reactants are linked together to form products.
- The enzyme dissociates from the formed molecules. That diffuses from the site of the reaction. And the enzyme regains its original configuration. And is ready to bind to another substrate molecule.
Many factors, including temperature, pH, and enzyme. And substrate concentrations, affect the rates of enzymatic reactions. And the presence of inhibitors.
Temperature and higher temperatures increase the rate of most chemical reactions. Because the molecules are moving faster. And this is not true of enzymatic enzymes. The active sites of enzymes change shape as the temperature changes. If the temperature is too high If it increases too much or decreases too much. Then the enzyme does not get enjoy its internal level.
Each enzyme has the greatest temperature for its activity. The greatest temperature for enzymes in the human body is 37°C, which is the normal body temperature. Some pathogens can cause disease in humans. One reason is that these microorganisms.
Also, have an enzyme greatest of 37 °C. Enzymes of some other microorganisms. But, work best at much higher temperatures; for hyperthermophiles. Such organisms can exceed 80 °C. but grows.
If the temperature rises beyond a certain point, non-covalent bonds. Within the enzyme are broken and the enzyme ceases to be used. The 3-dimensional structure is destroyed so they no longer have a functional conformation.
While enzymes are unable to return to their original three-dimensional structure. Such as when egg whites are cooked and then cooled. In other cases, the enzymes revert to The non-covalent bonds of the enzyme are re-formed. When the enzyme returns to normal.
Enzymes are denatured even at extremes of pH. When ions released from acids and bases interfere with hydrogen bonding. And become denatured and disrupts the secondary and tertiary structures of enzymes. Thus, each enzyme has the best pH.
Changing the pH can control the growth of unwanted microorganisms. By exploiting their proteins. For example, vinegar acts as a preservative in dill pickles, and ammonia is a disinfectant. Can be used as.
Enzyme and substrate concentration is Another factor that determines. The rate of enzymatic activity within cells is the concentration of the substrate. As the substrate concentration increases, enzymatic activity increases.
When more and more enzyme-active sites are present. Substrate molecules bind, s reach their saturation point. When all enzyme active sites are bound. And adding more substrate will no longer increase the rate of enzymatic activity.
Enzymatic activity is also affected by the concentration of enzymes in the cells. One-way organisms control their metabolism is to control the amount. And the timing of enzyme synthesis. In other words, many enzymes regulate metabolic activity.
These enzymes are produced in enough quantities to maintain them. And their metabolic activity is required to be maintained at these stages. Eukaryotic cells have few Enzymes that are regulated by the assembly of enzymes. Within the membrane, certain metabolic reactions occur.
Separated from the rest of the cell. For example, white blood cells transport phagocytized pathogens using enzymes packaged within lysosomes.
Enzymatic activity can be affected by a variety of substances. That block the active site of the enzyme. Enzymatic inhibitors, which are either competitive or non.
Competitive inhibition The shape of the inhibitor is designed to fit. Into the active site of the enzyme and thus inhibit the normal substrate. But, such inhibitors do not undergo.
A chemical reaction to form products from binding. Competitive inhibitors can bind to an active site either.
Permanent binding results in permanent loss of enzymatic activity. Reversible competition can be overcome by increasing the concentration of substrate molecules. Increasing the likelihood that the active sites will be filled.
With substrate rather than the inhibitor. An example of competitive inhibition is the action of sulfanilamide. Which has the same shape as para-aminobenzoic acid. Once sulfanilamide is bound to the enzyme, it remains bound. As a result.
Faniamide inhibits the bacteria sulfanilamide which makes folic acid. Humans do not synthesize folic acid. We must take it as a vitamin in our diet—so sulfanilamide does not affect us in this way.
Non-competitive inhibitors act not by binding to the active site. But by binding to an allosteric site located elsewhere. On the enzyme instead of the enzyme to inhibit enzymatic activity.
Binding to the allosteric site Alters the shape of the active site. That the substrate is not inhibited. Allosteric control of enzyme activity has two types of stimulatory and stimulatory effects.
Allosteric inhibition inhibits enzymatic activity in the manner described. Stimulatory allosteric activation In, binding of specific activating molecules. An allosteric site changes the shape of the active site.
Which activates an otherwise inactive enzyme. Some enzymes have an allosteric site. which are both inhibitory and stimulatory and regulate their function.
Cells control enzyme action by feedback inhibition. Allocation acts as feedback inhibition.
A thermostat controls the heater. When the room heats up. The sensor in the thermostat changes shape. And sends an electrical signal that turns the heater off. In metabolic reaction inhibition.
The end product of a series of reactions. First is the dissociative inhibitory of any enzyme in the pathway. Since the product of each reaction in the pathway is the substrate for the next reaction.
Inhibition of the first enzyme in the chain stops. The entire pathway thus conserves cell energy. For example, in Escherichia coli, permeation of the amino acid.
Isoleucine inhibits the first enzyme in the anabolic pathway that produces isoleucine. Thus, the bacterium inhibits the synthesis of isoleucine. When the amino acid is available. When isoleucine is degraded the enzyme is no longer resistant. And isoleucine production begins
Up to this point, we view the concept of metabolism as a collection of chemical reactions. That can be classified as either catabolic or anabolic. Because enzymes are involved in reducing the activation energy of these reactions. are required, we examined them in some detail.
Energy is also vital to metabolism, so we examined redox reactions. As a way to transfer energy within cells. For example, we saw redox reactions and the use of carrier molecules. To transfer energy from ATP which stores energy in the cells.
We will now consider how cells get and use metabolites. That are used to synthesize the micromolecules needed for growth. And finally to produce the end goal of metabolism i.e. final. We will consider in more detail the phosphorylation of APP to generate ATP.
Carbohydrate Catabolism
Although other sugars, amino acids, and fats are also used, they are first converted to glucose. Glucose can be catabolized by one of two processes—the process. By which cellular respiration converts glucose to carbon dioxide. And converts it with water or by fermentation.
Both cellular respiration and fermentation begin with glycolysis. A process that results in the catabolism of one molecule of glucose to two molecules of pyruvic acid. And a small amount of ATP production.
Respiration is then followed by the Krebs cycle and electron transport. Continues through the chain leading to a significant amount of ATP production. Fermentation causes pyruvic acid to be converted into other organic compounds. Fermentation causes much less ATP to be produced than respiration.
The following is a simplified discussion of glucose catabolism. To understand the basic reactions occurring. In each pathway of glucose catabolism, three things need to be taken into account.
The number of carbon molecules in each of the intermediate products. The relative number of ATP molecules, and the change in pH. As they get reduced and then oxidized back to their original form.
Glycolysis
Glycolysis, as scientists discovered. Is the first step in the catabolism of glucose through. Both respiration and fermentation. Glycolysis occurs in most cells. As its name implies, glycolysis involves the splitting of six carbon glucose molecules.
Into two involves splitting into sugar molecules. When these three-carbon molecules are oxidized. Pyruvic acid, some of them are stored.
